Advanced gum disease or "periodontitis" is an infection caused by bacteria that results in the loss of supporting tissues around teeth and the formation of periodontal pockets. Treatment for this condition include deep cleanings (called scaling and root planing) and antibiotic therapy. The purpose of this research study is to measure blood and saliva levels of antibiotic and to assess changes in gastrointestinal bacteria for subjects with periodontitis who are treated with a local antibiotic formulation. In this study, subjects with periodontitis will be conventionally treated with a deep cleaning. They will additionally be treated with a minocycline powder which will be placed under the gums within periodontal pockets. Minocycline HCl is an antibiotic related to tetracycline that is effective against many bacteria including those that cause advanced gum disease. The formulation used in this study is currently under investigation for approval by the FDA. Participation in this study will involve a one-night hospital stay and dental clinic visits over a 10-week period.